Enabling Distributed Collaboration among Heterogeneous Devices

ABSTRACT In this paper we describe a new class of collaborative scientific applications that incorporate heterogeneous devices, such as shared supercomputing or visualization resources, personal computers, and mobile devices, present some classes of collaboration tasks that could profitably make use an application infrastructure that connects heterogeneous devices, and identify some particular applications that fall into these classes. We also describe in greater detail one potential application, natural science field research that employs sensor networks. We also discuss some of the problems that need to be addressed in building an application that allows such heterogeneous device collaboration and some benefits to digital science that could be realized by building collaborative applications in this fashion

Editorial: Presence and beyond: Evaluating user experience in AR/MR/VR

The call for this Research Topic was intentionally broad: We sought papers that identify or propose constructs that can be used to describe AR/MR/VR, and papers that evaluate the utility of those constructs; we sought papers that discussed measures relating to user experience in AR/MR/VR - including, but not limited to, presence. In the end, we were very happy to publish fifteen articles addressing a variety of these questions - but, notably, not all of them. In the remainder of this editorial, we briefly introduce each of the fifteen articles, loosely grouping them into relevant categories. We then discuss each of the three categories in turn, and close with a call to action for our AR/MR/VR research community to more actively engage with human-computer interaction (HCI) and user experience (UX) researchers

The Integrated Virtual Environment Rehabilitation Treadmill System

Slow gait speed and interlimb asymmetry are prevalent in a variety of disorders. Current approaches to locomotor retraining emphasize the need for appropriate feedback during intensive, task-specific practice. This paper describes the design and feasibility testing of the integrated virtual environment rehabilitation treadmill (IVERT) system intended to provide real-time, intuitive feedback regarding gait speed and asymmetry during training. The IVERT system integrates an instrumented, split-belt treadmill with a front-projection, immersive virtual environment. The novel adaptive control system uses only ground reaction force data from the treadmill to continuously update the speeds of the two treadmill belts independently, as well as to control the speed and heading in the virtual environment in real time. Feedback regarding gait asymmetry is presented 1) visually as walking a curved trajectory through the virtual environment and 2) proprioceptively in the form of different belt speeds on the split-belt treadmill. A feasibility study involving five individuals with asymmetric gait found that these individuals could effectively control the speed of locomotion and perceive gait asymmetry during the training session. Although minimal changes in overground gait symmetry were observed immediately following a single training session, further studies should be done to determine the IVERT’s potential as a tool for rehabilitation of asymmetric gait by providing patients with congruent visual and proprioceptive feedback

Server‐side workflow execution using data grid technology for reproducible analyses of data‐intensive hydrologic systems

Many geoscience disciplines utilize complex computational models for advancing understanding and sustainable management of Earth systems. Executing such models and their associated data preprocessing and postprocessing routines can be challenging for a number of reasons including (1) accessing and preprocessing the large volume and variety of data required by the model, (2) postprocessing large data collections generated by the model, and (3) orchestrating data processing tools, each with unique software dependencies, into workflows that can be easily reproduced and reused. To address these challenges, the work reported in this paper leverages the Workflow Structured Object functionality of the Integrated Rule‐Oriented Data System and demonstrates how it can be used to access distributed data, encapsulate hydrologic data processing as workflows, and federate with other community‐driven cyberinfrastructure systems. The approach is demonstrated for a study investigating the impact of drought on populations in the Carolinas region of the United States. The analysis leverages computational modeling along with data from the Terra Populus project and data management and publication services provided by the Sustainable Environment‐Actionable Data project. The work is part of a larger effort under the DataNet Federation Consortium project that aims to demonstrate data and computational interoperability across cyberinfrastructure developed independently by scientific communities.Plain Language SummaryExecuting computational workflows in the geosciences can be challenging, especially when dealing with large, distributed, and heterogeneous data sets and computational tools. We present a methodology for addressing this challenge using the Integrated Rule‐Oriented Data System (iRODS) Workflow Structured Object (WSO). We demonstrate the approach through an end‐to‐end application of data access, processing, and publication of digital assets for a scientific study analyzing drought in the Carolinas region of the United States.Key PointsReproducibility of data‐intensive analyses remains a significant challengeData grids are useful for reproducibility of workflows requiring large, distributed data setsData and computations should be co‐located on servers to create executable Web‐resourcesPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137520/1/ess271_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137520/2/ess271.pd

Erg-O: ergonomic optimization of immersive virtual environments

Interaction in VR involves large body movements, easily inducing fatigue and discomfort. We propose Erg-O, a manipulation technique that leverages visual dominance to maintain the visual location of the elements in VR, while making them accessible from more comfortable locations. Our solution works in an open-ended fashion (no prior knowledge of the object the user wants to touch), can be used with multiple objects, and still allows interaction with any other point within user's reach. We use optimization approaches to compute the best physical location to interact with each visual element, and space partitioning techniques to distort the visual and physical spaces based on those mappings and allow multi-object retargeting. In this paper we describe the Erg-O technique, propose two retargeting strategies and report the results from a user study on 3D selection under different conditions, elaborating on their potential and application to specific usage scenarios

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field